[med-svn] [Git][med-team/probcons][master] 6 commits: Merge `probcons-extra` in `probcons`.
Charles Plessy (@plessy)
gitlab at salsa.debian.org
Fri Aug 7 02:52:34 BST 2026
Charles Plessy pushed to branch master at Debian Med / probcons
Commits:
9694f8da by Charles Plessy at 2026-08-07T09:26:48+09:00
Merge `probcons-extra` in `probcons`.
Both packages are tiny; we do not need this kind of complication
anymore.
Note to self:
for f in *xml ; do xsltproc --nonet /usr/share/xml/docbook/stylesheet/docbook-xsl/manpages/docbook.xsl $f; done
- - - - -
00874018 by Charles Plessy at 2026-08-07T09:54:17+09:00
Remove mention of the PDF manual that we stopped shipping 20 years ago.
Closes: #1143830
- - - - -
f9c6c4ba by Charles Plessy at 2026-08-07T10:01:16+09:00
Update standards version to 4.7.4, no changes needed.
Upgrade checklist verified:
4.7.3 → 4.7.4:
* Package is not in non-free-firmware
Changes-By: lintian-brush
Fixes: lintian: out-of-date-standards-version
See-also: https://lintian.debian.org/tags/out-of-date-standards-version.html
- - - - -
c84fd2d4 by Charles Plessy at 2026-08-07T10:48:37+09:00
Changes made by cme
- - - - -
246bd55b by Charles Plessy at 2026-08-07T10:48:40+09:00
Drop 'Rules-Requires-Root: no' from d/control (routine-update)
- - - - -
9585f9c4 by Charles Plessy at 2026-08-07T10:50:26+09:00
routine-update: Ready to upload to unstable
- - - - -
20 changed files:
- debian/README.Debian
- debian/changelog
- debian/control
- debian/pc-compare.1
- debian/pc-compare.1.xml
- debian/pc-makegnuplot.1
- debian/pc-makegnuplot.1.xml
- debian/pc-project.1
- debian/pc-project.1.xml
- debian/probcons-RNA.1
- debian/probcons-RNA.1.xml
- − debian/probcons-extra.dirs
- − debian/probcons-extra.install
- − debian/probcons-extra.manpages
- debian/probcons.1
- debian/probcons.1.xml
- debian/probcons.dirs
- debian/probcons.install
- debian/probcons.manpages
- debian/rules
Changes:
=====================================
debian/README.Debian
=====================================
@@ -1,9 +1,9 @@
probcons for Debian
-------------------
-* The "compare", "project" and "makegnuplot" programs are located in the
- probcons-extra package and renamed "pc-compare", "pc-project" and
- "pc-makegnuplot" to avoid collision with other program names.
+* The `compare`, `project` and `makegnuplot` programs were renamed
+ `pc-compare`, `pc-project` and `pc-makegnuplot` to avoid collision with
+ other program names.
* This package contains an additional binary which is not in the original
distribution of ProbCons: probcons-RNA. It is an experimental version of
@@ -12,4 +12,4 @@ probcons for Debian
http://probcons.stanford.edu/probconsRNA.tar.gz, and the current version of
probcons was used to build probcons-RNA.
- -- Charles Plessy <charles-debian-nospam at plessy.org>, Wed, 18 Apr 2007 22:30:52 +0900
+ -- Charles Plessy <charles-debian-nospam at plessy.org>, Fri, 07 Aug 2026 09:06:30 +0900
=====================================
debian/changelog
=====================================
@@ -1,3 +1,15 @@
+probcons (1.12-16) unstable; urgency=medium
+
+ * Merge `probcons-extra` in `probcons`.
+ * Remove mention of the PDF manual that stopped shipping 20 years ago.
+ Closes: #1143830
+ * Update standards version to 4.7.4, no changes needed.
+ * Reflow Uploaders field (cme)
+ * Remove Priority field (cme)
+ * Drop 'Rules-Requires-Root: no' from d/control (routine-update)
+
+ -- Charles Plessy <plessy at debian.org> Fri, 07 Aug 2026 10:48:53 +0900
+
probcons (1.12-15) unstable; urgency=medium
* Team upload.
=====================================
debian/control
=====================================
@@ -1,22 +1,31 @@
Source: probcons
+Standards-Version: 4.7.4
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
-Uploaders: Charles Plessy <plessy at debian.org>,
- Andreas Tille <tille at debian.org>
+Uploaders:
+ Charles Plessy <plessy at debian.org>,
+ Andreas Tille <tille at debian.org>,
Section: science
-Priority: optional
-Build-Depends: debhelper-compat (= 13)
-Standards-Version: 4.7.2
+Build-Depends:
+ debhelper-compat (= 13),
Vcs-Browser: https://salsa.debian.org/med-team/probcons
Vcs-Git: https://salsa.debian.org/med-team/probcons.git
Homepage: http://probcons.stanford.edu/
-Rules-Requires-Root: no
Package: probcons
Architecture: any
-Depends: ${shlibs:Depends},
- ${misc:Depends}
-Suggests: probcons-extra
-Enhances: t-coffee
+Depends:
+ ${shlibs:Depends},
+ ${misc:Depends},
+Suggests:
+ gnuplot-nox | gnuplot-x11,
+Enhances:
+ t-coffee,
+Breaks:
+ probcons-extra,
+Provides:
+ probcons-extra,
+Replaces:
+ probcons-extra,
Description: PROBabilistic CONSistency-based multiple sequence alignment
Tool for generating multiple alignments of protein sequences. Using a
combination of probabilistic modeling and consistency-based alignment
@@ -26,19 +35,3 @@ Description: PROBabilistic CONSistency-based multiple sequence alignment
programs, containing an average of 7% more correctly aligned columns than
those of T-Coffee, 11% more correctly aligned columns than those of CLUSTAL W,
and 14% more correctly aligned columns than those of DIALIGN.
-
-Package: probcons-extra
-Architecture: any
-Depends: probcons (= ${binary:Version}),
- ${shlibs:Depends},
- ${misc:Depends}
-Suggests: gnuplot-nox | gnuplot-x11
-Description: Extra programs from the probcons package
- Contains the convert, project and makgnuplot programs from the probcons
- package, which have been renamed to pc-compare, pc-project and pc-makegnuplot
- respectively to avoid collisions with other program names. These programs are
- mostly useful for testing purposes and are not required for the normal usage of
- Probcons.
- .
- Probcons is a tool for generating multiple alignments of protein
- sequences.
=====================================
debian/pc-compare.1
=====================================
@@ -1,49 +1,65 @@
+'\" t
.\" Title: PC-COMPARE
.\" Author: Chuong Do <chuongdo at cs.stanford.edu>
-.\" Generator: DocBook XSL Stylesheets v1.73.2 <http://docbook.sf.net/>
+.\" Generator: DocBook XSL Stylesheets vsnapshot <http://docbook.sf.net/>
.\" Date: 2007-04-04
.\" Manual: Probcons Manual
.\" Source: pc-compare 1.12
+.\" Language: English
.\"
.TH "PC\-COMPARE" "1" "2007\-04\-04" "pc-compare 1.12" "Probcons Manual"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
.\" disable hyphenation
.nh
.\" disable justification (adjust text to left margin only)
.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
.SH "NAME"
-pc-compare - Program for scoring alignments according to a reference alignment with respect to sum-of-pairs and column scores.
+pc-compare \- Program for scoring alignments according to a reference alignment with respect to sum\-of\-pairs and column scores\&.
.SH "SYNOPSIS"
-.HP 11
+.HP \w'\fBpc\-compare\fR\ 'u
\fBpc\-compare\fR [\fITEST_ALIGNMENT\fR] [\fIREFERENCE_ALIGNMENT\fR] [\fIBALIBASE_ANNOT_FILE\fR] [\fB\-col\fR] [\fB\-core\fR] [\fB\-caps\fR] [\fB\-annot\ \fR\fB\fIFILENAME\fR\fR]
.SH "NOTE"
.PP
pc\-compare is named
-\fIcompare\fR
-in the original sources, but has been remamed to avoid collision with other program names\.
+compare
+in the original sources, but has been remamed to avoid collision with other program names\&.
.SH "SEE ALSO"
.PP
-
\fBpc-makegnufile\fR(1),
-\fBpc-project\fR(1),from the probcons\-extra package, and
+\fBpc-project\fR(1),
\fBprobcons\fR(1)
and
-\fBprobcons-RNA\fR(1)
-from the probcons package\.
+\fBprobcons-RNA\fR(1)\&.
.SH "REFERENCE"
.PP
-Please cite Do, C\.B\., Mahabhashyam, M\.S\.P\., Brudno, M\., and Batzoglou, S\. 2005\. PROBCONS: Probabilistic Consistency\-based Multiple Sequence Alignment\. Genome Research 15: 330\-340\.
+Please cite Do, C\&.B\&., Mahabhashyam, M\&.S\&.P\&., Brudno, M\&., and Batzoglou, S\&. 2005\&. PROBCONS: Probabilistic Consistency\-based Multiple Sequence Alignment\&. Genome Research 15: 330\-340\&.
.SH "AUTHORS"
.PP
-\fBChuong Do\fR <\&chuongdo at cs\.stanford\.edu\&>
-.sp -1n
-.IP "" 4
-Wrote probcons in collaboration with Michael Brudno in the research group of Serafim Batzoglou, Department of Computer Science, Stanford University\.
+\fBChuong Do\fR <\&chuongdo at cs\&.stanford\&.edu\&>
+.RS 4
+Wrote probcons in collaboration with Michael Brudno in the research group of Serafim Batzoglou, Department of Computer Science, Stanford University\&.
+.RE
.PP
-\fBCharles Plessy\fR <\&charles\-debian\-nospam at plessy\.org\&>
-.sp -1n
-.IP "" 4
-Wrote this manpage in DocBook XML for the Debian distribution\.
+\fBCharles Plessy\fR <\&charles\-debian\-nospam at plessy\&.org\&>
+.RS 4
+Wrote this manpage in DocBook XML for the Debian distribution\&.
+.RE
.SH "COPYRIGHT"
+.br
.PP
-This program and its manpage are in the public domain\.
+This program and its manpage are in the public domain\&.
.sp
=====================================
debian/pc-compare.1.xml
=====================================
@@ -102,7 +102,7 @@
<citerefentry>
<refentrytitle>pc-project</refentrytitle>
<manvolnum>1</manvolnum>
- </citerefentry>,from the probcons-extra package, and
+ </citerefentry>,
<citerefentry>
<refentrytitle>probcons</refentrytitle>
<manvolnum>1</manvolnum>
@@ -110,7 +110,7 @@
<citerefentry>
<refentrytitle>probcons-RNA</refentrytitle>
<manvolnum>1</manvolnum>
- </citerefentry> from the probcons package.</para>
+ </citerefentry>.</para>
</refsect1>
<refsect1>
=====================================
debian/pc-makegnuplot.1
=====================================
@@ -1,49 +1,65 @@
+'\" t
.\" Title: PC-MAKEGNUPLOT
.\" Author: Chuong Do <chuongdo at cs.stanford.edu>
-.\" Generator: DocBook XSL Stylesheets v1.73.2 <http://docbook.sf.net/>
+.\" Generator: DocBook XSL Stylesheets vsnapshot <http://docbook.sf.net/>
.\" Date: 2007-04-04
.\" Manual: Probcons Manual
.\" Source: pc-makegnuplot 1.12
+.\" Language: English
.\"
.TH "PC\-MAKEGNUPLOT" "1" "2007\-04\-04" "pc-makegnuplot 1.12" "Probcons Manual"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
.\" disable hyphenation
.nh
.\" disable justification (adjust text to left margin only)
.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
.SH "NAME"
-pc-makegnuplot - Utility to plot annotation scores.
+pc-makegnuplot \- Utility to plot annotation scores\&.
.SH "SYNOPSIS"
-.HP 15
+.HP \w'\fBpc\-makegnuplot\fR\ 'u
\fBpc\-makegnuplot\fR [\fIannotscores\fR] [\-refscores]
.SH "NOTE"
.PP
pc\-makegnuplot is named
-\fImakegnuplot\fR
-in the original sources, but has been remamed to avoid collision with other program names\.
+makegnuplot
+in the original sources, but has been remamed to avoid collision with other program names\&.
.SH "SEE ALSO"
.PP
-
\fBpc-compare\fR(1),
-\fBpc-project\fR(1),from the probcons\-extra package, and
+\fBpc-project\fR(1),
\fBprobcons\fR(1)
and
-\fBprobcons-RNA\fR(1)
-from the probcons package\.
+\fBprobcons-RNA\fR(1)\&.
.SH "REFERENCE"
.PP
-Please cite Do, C\.B\., Mahabhashyam, M\.S\.P\., Brudno, M\., and Batzoglou, S\. 2005\. PROBCONS: Probabilistic Consistency\-based Multiple Sequence Alignment\. Genome Research 15: 330\-340\.
+Please cite Do, C\&.B\&., Mahabhashyam, M\&.S\&.P\&., Brudno, M\&., and Batzoglou, S\&. 2005\&. PROBCONS: Probabilistic Consistency\-based Multiple Sequence Alignment\&. Genome Research 15: 330\-340\&.
.SH "AUTHORS"
.PP
-\fBChuong Do\fR <\&chuongdo at cs\.stanford\.edu\&>
-.sp -1n
-.IP "" 4
-Wrote probcons in collaboration with Michael Brudno in the research group of Serafim Batzoglou, Department of Computer Science, Stanford University\.
+\fBChuong Do\fR <\&chuongdo at cs\&.stanford\&.edu\&>
+.RS 4
+Wrote probcons in collaboration with Michael Brudno in the research group of Serafim Batzoglou, Department of Computer Science, Stanford University\&.
+.RE
.PP
-\fBCharles Plessy\fR <\&charles\-debian\-nospam at plessy\.org\&>
-.sp -1n
-.IP "" 4
-Wrote this manpage in DocBook XML for the Debian distribution\.
+\fBCharles Plessy\fR <\&charles\-debian\-nospam at plessy\&.org\&>
+.RS 4
+Wrote this manpage in DocBook XML for the Debian distribution\&.
+.RE
.SH "COPYRIGHT"
+.br
.PP
-This program and its manpage are in the public domain\.
+This program and its manpage are in the public domain\&.
.sp
=====================================
debian/pc-makegnuplot.1.xml
=====================================
@@ -93,7 +93,7 @@
<citerefentry>
<refentrytitle>pc-project</refentrytitle>
<manvolnum>1</manvolnum>
- </citerefentry>,from the probcons-extra package, and
+ </citerefentry>,
<citerefentry>
<refentrytitle>probcons</refentrytitle>
<manvolnum>1</manvolnum>
@@ -101,7 +101,7 @@
<citerefentry>
<refentrytitle>probcons-RNA</refentrytitle>
<manvolnum>1</manvolnum>
- </citerefentry> from the probcons package.</para>
+ </citerefentry>.</para>
</refsect1>
<refsect1>
=====================================
debian/pc-project.1
=====================================
@@ -1,49 +1,65 @@
+'\" t
.\" Title: PC-PROJECT
.\" Author: Chuong Do <chuongdo at cs.stanford.edu>
-.\" Generator: DocBook XSL Stylesheets v1.73.2 <http://docbook.sf.net/>
+.\" Generator: DocBook XSL Stylesheets vsnapshot <http://docbook.sf.net/>
.\" Date: 2007-04-04
.\" Manual: Probcons Manual
.\" Source: pc-project 1.12
+.\" Language: English
.\"
.TH "PC\-PROJECT" "1" "2007\-04\-04" "pc-project 1.12" "Probcons Manual"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
.\" disable hyphenation
.nh
.\" disable justification (adjust text to left margin only)
.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
.SH "NAME"
-pc-project - Program to project multiple alignment to pairwise alignments.
+pc-project \- Program to project multiple alignment to pairwise alignments\&.
.SH "SYNOPSIS"
-.HP 11
+.HP \w'\fBpc\-project\fR\ 'u
\fBpc\-project\fR [\fIALIGNMENT\fR] [\-nocompressgaps]
.SH "NOTE"
.PP
pc\-project is named
-\fIproject\fR
-in the original sources, but has been remamed to avoid collision with other program names\.
+project
+in the original sources, but has been remamed to avoid collision with other program names\&.
.SH "SEE ALSO"
.PP
-
\fBpc-makegnufile\fR(1),
-\fBpc-compare\fR(1),from the probcons\-extra package, and
+\fBpc-compare\fR(1),
\fBprobcons\fR(1)
and
-\fBprobcons-RNA\fR(1)
-from the probcons package\.
+\fBprobcons-RNA\fR(1)\&.
.SH "REFERENCE"
.PP
-Please cite Do, C\.B\., Mahabhashyam, M\.S\.P\., Brudno, M\., and Batzoglou, S\. 2005\. PROBCONS: Probabilistic Consistency\-based Multiple Sequence Alignment\. Genome Research 15: 330\-340\.
+Please cite Do, C\&.B\&., Mahabhashyam, M\&.S\&.P\&., Brudno, M\&., and Batzoglou, S\&. 2005\&. PROBCONS: Probabilistic Consistency\-based Multiple Sequence Alignment\&. Genome Research 15: 330\-340\&.
.SH "AUTHORS"
.PP
-\fBChuong Do\fR <\&chuongdo at cs\.stanford\.edu\&>
-.sp -1n
-.IP "" 4
-Wrote probcons in collaboration with Michael Brudno in the research group of Serafim Batzoglou, Department of Computer Science, Stanford University\.
+\fBChuong Do\fR <\&chuongdo at cs\&.stanford\&.edu\&>
+.RS 4
+Wrote probcons in collaboration with Michael Brudno in the research group of Serafim Batzoglou, Department of Computer Science, Stanford University\&.
+.RE
.PP
-\fBCharles Plessy\fR <\&charles\-debian\-nospam at plessy\.org\&>
-.sp -1n
-.IP "" 4
-Wrote this manpage in DocBook XML for the Debian distribution\.
+\fBCharles Plessy\fR <\&charles\-debian\-nospam at plessy\&.org\&>
+.RS 4
+Wrote this manpage in DocBook XML for the Debian distribution\&.
+.RE
.SH "COPYRIGHT"
+.br
.PP
-This program and its manpage are in the public domain\.
+This program and its manpage are in the public domain\&.
.sp
=====================================
debian/pc-project.1.xml
=====================================
@@ -95,7 +95,7 @@
<citerefentry>
<refentrytitle>pc-compare</refentrytitle>
<manvolnum>1</manvolnum>
- </citerefentry>,from the probcons-extra package, and
+ </citerefentry>,
<citerefentry>
<refentrytitle>probcons</refentrytitle>
<manvolnum>1</manvolnum>
@@ -103,7 +103,7 @@
<citerefentry>
<refentrytitle>probcons-RNA</refentrytitle>
<manvolnum>1</manvolnum>
- </citerefentry> from the probcons package.</para>
+ </citerefentry>.</para>
</refsect1>
<refsect1>
=====================================
debian/probcons-RNA.1
=====================================
@@ -1,51 +1,69 @@
+'\" t
.\" Title: PROBCONS-RNA
.\" Author: Chuong Do <chuongdo at cs.stanford.edu>
-.\" Generator: DocBook XSL Stylesheets v1.73.2 <http://docbook.sf.net/>
+.\" Generator: DocBook XSL Stylesheets vsnapshot <http://docbook.sf.net/>
.\" Date: 2007-04-04
.\" Manual: Probcons Manual
.\" Source: probcons-RNA 1.12
+.\" Language: English
.\"
.TH "PROBCONS\-RNA" "1" "2007\-04\-04" "probcons-RNA 1.12" "Probcons Manual"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
.\" disable hyphenation
.nh
.\" disable justification (adjust text to left margin only)
.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
.SH "NAME"
-probcons-RNA - An experimental version of ProbCons compiled with parameters estimated via unsupervised training on BRAliBASE.
+probcons-RNA \- An experimental version of ProbCons compiled with parameters estimated via unsupervised training on BRAliBASE\&.
.SH "DESCRIPTION"
.PP
See the manpage of
\fBprobcons\fR(1)
for the command\-line arguments, and
-\fI/usr/share/doc/README\.Debian\fR
-for more information about how probcons\-RNA has been built\.
+/usr/share/doc/README\&.Debian
+for more information about how probcons\-RNA has been built\&.
.SH "SEE ALSO"
.sp
.RS 4
-\h'-04'\(bu\h'+03'You can find more information in the manual of ProbCons, which is located in
-\fI/usr/share/doc/probcons/manual\.pdf\fR
-in Debian systems\.
-.RE
-.sp
-.RS 4
-\h'-04'\(bu\h'+03'
+.ie n \{\
+\h'-04'\(bu\h'+03'\c
+.\}
+.el \{\
+.sp -1
+.IP \(bu 2.3
+.\}
\fBprobcons\fR(1),
\fBpc-makegnufile\fR(1),
\fBpc-compare\fR(1),
-\fBpc-project\fR(1), which are distributed separately in the probcons\-extra package\.
+\fBpc-project\fR(1)\&.
.RE
.SH "AUTHORS"
.PP
-\fBChuong Do\fR <\&chuongdo at cs\.stanford\.edu\&>
-.sp -1n
-.IP "" 4
-Wrote probcons in collaboration with Michael Brudno in the research group of Serafim Batzoglou, Department of Computer Science, Stanford University\.
+\fBChuong Do\fR <\&chuongdo at cs\&.stanford\&.edu\&>
+.RS 4
+Wrote probcons in collaboration with Michael Brudno in the research group of Serafim Batzoglou, Department of Computer Science, Stanford University\&.
+.RE
.PP
-\fBCharles Plessy\fR <\&charles\-debian\-nospam at plessy\.org\&>
-.sp -1n
-.IP "" 4
-Wrote this manpage in DocBook XML for the Debian distribution\.
+\fBCharles Plessy\fR <\&charles\-debian\-nospam at plessy\&.org\&>
+.RS 4
+Wrote this manpage in DocBook XML for the Debian distribution\&.
+.RE
.SH "COPYRIGHT"
+.br
.PP
-This program and its manpage are in the public domain\.
+This program and its manpage are in the public domain\&.
.sp
=====================================
debian/probcons-RNA.1.xml
=====================================
@@ -80,8 +80,6 @@
<refsect1>
<title>SEE ALSO</title>
<itemizedlist>
- <listitem><para>You can find more information in the manual of ProbCons, which is located in <filename>/usr/share/doc/probcons/manual.pdf</filename> in Debian systems.</para></listitem>
-
<listitem>
<para>
<citerefentry>
@@ -99,8 +97,7 @@
<citerefentry>
<refentrytitle>pc-project</refentrytitle>
<manvolnum>1</manvolnum>
- </citerefentry>,
- which are distributed separately in the probcons-extra package.</para></listitem>
+ </citerefentry>.</para></listitem>
</itemizedlist>
</refsect1>
=====================================
debian/probcons-extra.dirs deleted
=====================================
@@ -1,2 +0,0 @@
-usr/bin
-usr/share/doc
=====================================
debian/probcons-extra.install deleted
=====================================
@@ -1,4 +0,0 @@
-pc-project usr/bin/
-pc-makegnuplot usr/bin/
-pc-compare usr/bin/
-
=====================================
debian/probcons-extra.manpages deleted
=====================================
@@ -1,3 +0,0 @@
-debian/pc-makegnuplot.1
-debian/pc-compare.1
-debian/pc-project.1
=====================================
debian/probcons.1
=====================================
@@ -1,27 +1,44 @@
+'\" t
.\" Title: PROBCONS
.\" Author: Chuong Do <chuongdo at cs.stanford.edu>
-.\" Generator: DocBook XSL Stylesheets v1.73.2 <http://docbook.sf.net/>
+.\" Generator: DocBook XSL Stylesheets vsnapshot <http://docbook.sf.net/>
.\" Date: 2007-04-04
.\" Manual: Probcons Manual
.\" Source: probcons 1.12
+.\" Language: English
.\"
.TH "PROBCONS" "1" "2007\-04\-04" "probcons 1.12" "Probcons Manual"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
.\" disable hyphenation
.nh
.\" disable justification (adjust text to left margin only)
.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
.SH "NAME"
-probcons - align multiple protein sequences and print to standard output
+probcons \- align multiple protein sequences and print to standard output
.SH "SYNOPSIS"
-.HP 9
+.HP \w'\fBprobcons\fR\ 'u
\fBprobcons\fR [\fB\fIOPTION\fR\fR] [\fIMFAFILE\fR] [\fIMFAFILE\fR]
.SH "DESCRIPTION"
.PP
\fBprobcons\fR
-is a tool for generating multiple alignments of protein sequences\. Using a combination of probabilistic modeling and consistency\-based alignment techniques, PROBCONS has achieved the highest accuracies of all alignment methods to date\. On the BAliBASE benchmark alignment database, alignments produced by PROBCONS show statistically significant improvement over current programs, containing an average of 7% more correctly aligned columns than those of T\-Coffee, 11% more correctly aligned columns than those of CLUSTAL W, and 14% more correctly aligned columns than those of DIALIGN\.
+is a tool for generating multiple alignments of protein sequences\&. Using a combination of probabilistic modeling and consistency\-based alignment techniques, PROBCONS has achieved the highest accuracies of all alignment methods to date\&. On the BAliBASE benchmark alignment database, alignments produced by PROBCONS show statistically significant improvement over current programs, containing an average of 7% more correctly aligned columns than those of T\-Coffee, 11% more correctly aligned columns than those of CLUSTAL W, and 14% more correctly aligned columns than those of DIALIGN\&.
.PP
\fBprobcons\fR
-aligns sequences provided in MFA format\. This format consists of multiple sequences\. Each sequence in MFA format begins with a single\-line description, followed by lines of sequence data\. The description line is distinguished from the sequence data by a greater\-than (\(lq>\(rq) symbol in the first column\.
+aligns sequences provided in MFA format\&. This format consists of multiple sequences\&. Each sequence in MFA format begins with a single\-line description, followed by lines of sequence data\&. The description line is distinguished from the sequence data by a greater\-than (\(lq>\(rq) symbol in the first column\&.
.SH "OPTIONS"
.PP
\fB\-clustalw\fR
@@ -66,16 +83,16 @@ use Viterbi algorithm to generate all pairs (automatically enables
Report progress while aligning (default: off)
.RE
.PP
-\fB\-annot\fR \fIFILENAME\fR
+\fB\-annot\fR FILENAME
.RS 4
write annotation for multiple alignment to
-\fIFILENAME\fR
+FILENAME
.RE
.PP
-\fB\-t\fR \fB\-\-train\fR \fIFILENAME\fR
+\fB\-t\fR \fB\-\-train\fR FILENAME
.RS 4
compute EM transition probabilities, store in
-\fIFILENAME\fR
+FILENAME
(default: no training)
.RE
.PP
@@ -84,10 +101,10 @@ compute EM transition probabilities, store in
also reestimate emission probabilities (default: off)
.RE
.PP
-\fB\-p\fR \fB\-\-paramfile\fR \fIFILENAME\fR
+\fB\-p\fR \fB\-\-paramfile\fR FILENAME
.RS 4
read parameters from
-\fIFILENAME\fR
+FILENAME
(default: )
.RE
.PP
@@ -98,37 +115,45 @@ print sequences in alignment order rather than input order (default: off)
.SH "SEE ALSO"
.sp
.RS 4
-\h'-04'\(bu\h'+03'You can find more information in the manual of ProbCons, which is located in
-\fI/usr/share/doc/probcons/manual\.pdf\fR
-in Debian systems\.
+.ie n \{\
+\h'-04'\(bu\h'+03'\c
+.\}
+.el \{\
+.sp -1
+.IP \(bu 2.3
+.\}
+An experimental version of ProbCons compiled with parameters estimated via unsupervised training on BRAliBASE,
+\fBprobcons-RNA\fR(1), is also distributed in the ProbCons Debian package\&.
.RE
.sp
.RS 4
-\h'-04'\(bu\h'+03'An experimental version of ProbCons compiled with parameters estimated via unsupervised training on BRAliBASE,
-\fBprobcons-RNA\fR(1), is also distributed in the ProbCons Debian package\.
-.RE
-.sp
-.RS 4
-\h'-04'\(bu\h'+03'
+.ie n \{\
+\h'-04'\(bu\h'+03'\c
+.\}
+.el \{\
+.sp -1
+.IP \(bu 2.3
+.\}
\fBpc-makegnufile\fR(1),
\fBpc-compare\fR(1),
-\fBpc-project\fR(1), which are distributed separately in the probcons\-extra package\.
+\fBpc-project\fR(1)\&.
.RE
.SH "REFERENCE"
.PP
-Please cite Do, C\.B\., Mahabhashyam, M\.S\.P\., Brudno, M\., and Batzoglou, S\. 2005\. PROBCONS: Probabilistic Consistency\-based Multiple Sequence Alignment\. Genome Research 15: 330\-340\.
+Please cite Do, C\&.B\&., Mahabhashyam, M\&.S\&.P\&., Brudno, M\&., and Batzoglou, S\&. 2005\&. PROBCONS: Probabilistic Consistency\-based Multiple Sequence Alignment\&. Genome Research 15: 330\-340\&.
.SH "AUTHORS"
.PP
-\fBChuong Do\fR <\&chuongdo at cs\.stanford\.edu\&>
-.sp -1n
-.IP "" 4
-Wrote probcons in collaboration with Michael Brudno in the research group of Serafim Batzoglou, Department of Computer Science, Stanford University\.
+\fBChuong Do\fR <\&chuongdo at cs\&.stanford\&.edu\&>
+.RS 4
+Wrote probcons in collaboration with Michael Brudno in the research group of Serafim Batzoglou, Department of Computer Science, Stanford University\&.
+.RE
.PP
-\fBCharles Plessy\fR <\&charles\-debian\-nospam at plessy\.org\&>
-.sp -1n
-.IP "" 4
-Wrote this manpage in DocBook XML for the Debian distribution\.
+\fBCharles Plessy\fR <\&charles\-debian\-nospam at plessy\&.org\&>
+.RS 4
+Wrote this manpage in DocBook XML for the Debian distribution\&.
+.RE
.SH "COPYRIGHT"
+.br
.PP
-This program and its manpage are in the public domain\.
+This program and its manpage are in the public domain\&.
.sp
=====================================
debian/probcons.1.xml
=====================================
@@ -203,8 +203,6 @@
<refsect1>
<title>SEE ALSO</title>
<itemizedlist>
- <listitem><para>You can find more information in the manual of ProbCons, which is located in <filename>/usr/share/doc/probcons/manual.pdf</filename> in Debian systems.</para></listitem>
-
<listitem><para>An experimental version of ProbCons compiled with parameters estimated via unsupervised training on BRAliBASE, <citerefentry><refentrytitle>probcons-RNA</refentrytitle><manvolnum>1</manvolnum></citerefentry>, is also distributed in the ProbCons Debian package.</para></listitem>
<listitem>
@@ -220,8 +218,7 @@
<citerefentry>
<refentrytitle>pc-project</refentrytitle>
<manvolnum>1</manvolnum>
- </citerefentry>,
- which are distributed separately in the probcons-extra package.</para></listitem>
+ </citerefentry>.</para></listitem>
</itemizedlist>
</refsect1>
=====================================
debian/probcons.dirs
=====================================
@@ -1,3 +1,5 @@
usr/bin
usr/share/doc
usr/share/doc/probcons
+usr/bin
+usr/share/doc
=====================================
debian/probcons.install
=====================================
@@ -1,2 +1,6 @@
probcons usr/bin/
probcons-RNA usr/bin/
+pc-project usr/bin/
+pc-makegnuplot usr/bin/
+pc-compare usr/bin/
+
=====================================
debian/probcons.manpages
=====================================
@@ -1,2 +1,5 @@
debian/probcons.1
debian/probcons-RNA.1
+debian/pc-makegnuplot.1
+debian/pc-compare.1
+debian/pc-project.1
=====================================
debian/rules
=====================================
@@ -13,10 +13,6 @@ override_dh_auto_build:
cp debian/Defaults-RNA.h Defaults-RNA.h
dh_auto_build
-override_dh_link:
- rm -rf $(CURDIR)/debian/probcons-extra/usr/share/doc/probcons-extra
- dh_link -p probcons-extra usr/share/doc/probcons usr/share/doc/probcons-extra
-
override_dh_clean:
dh_clean $(BINARIES) Main-RNA.cc Defaults-RNA.h
View it on GitLab: https://salsa.debian.org/med-team/probcons/-/compare/347edb49bac6f47b26a3571976828c7b244f6589...9585f9c4754add68afcfc1a90b44afb0767b8ddb
--
View it on GitLab: https://salsa.debian.org/med-team/probcons/-/compare/347edb49bac6f47b26a3571976828c7b244f6589...9585f9c4754add68afcfc1a90b44afb0767b8ddb
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